ZBTB38
protein-codingzinc finger and BTB domain containing 38, the group of Zinc fingers C2H2-type|BTB domain containing
Gene summary
The protein encoded by this gene is a zinc finger transcriptional activator that binds methylated DNA. The encoded protein can form homodimers or heterodimers through the zinc finger domains. In mouse, inhibition of this protein has been associated with apoptosis in some cell types. [provided by RefSeq, Jun 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~125.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ZBTB38 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001376113.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | 4 | |||
| missense | 110 | 8 | 2 | 120 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 110 | 10 | 4 | 124 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001363042.1 | 1 | MANE Select | |
| Ensembl | ENSP00000372635.5 | 1 | MANE Select | |
| RefSeq | NP_001073881.2 | 1 | Standard | |
| RefSeq | NP_001337028.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of DNA replication
- regulation of transcription, DNA-templated
- cellular response to DNA damage stimulus
- negative regulation of transcription, DNA-templated
- positive regulation of transcription by RNA polymerase II
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- DNA-binding transcription factor activity
- protein binding
- methyl-CpG binding
Cellular Component
- nucleus
- nucleoplasm
- chromosome
- blood microparticle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000514251
- Coding exons
- 1
- Length
- 125580
- Individuals with no LoFs
- 124756
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 124761
- p
- 0.0000200
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.31 | 494 | 661 | 0.747 | 0.0000364 | 7956 |
| Missense (PolyPhen) | 125 | 264.46 | 0.47267 | 3243 | ||
| Synonymous | 1.52 | 227 | 258 | 0.879 | 0.0000161 | 2260 |
| Loss of Function | 5.02 | 3 | 35.1 | 0.0856 | 0.00000195 | 468 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcriptional regulator with bimodal DNA-binding specificity. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to E-box elements (5'-CACGTG-3'). Can also bind specifically to a single methyl-CpG pair. Represses transcription in a methyl- CpG-dependent manner (PubMed:16354688). Plays an important role in regulating DNA replication and common fragile sites (CFS) stability in a RBBP6- and MCM10-dependent manner; represses expression of MCM10 which plays an important role in DNA- replication (PubMed:24726359). Acts as a transcriptional activator. May be involved in the differentiation and/or survival of late postmitotic neurons (By similarity). {ECO:0000250|UniProtKB:Q5EXX3, ECO:0000269|PubMed:16354688, ECO:0000269|PubMed:24726359}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.0810
- RVIS EVS
- 0.03
- RVIS percentile EVS
- 55.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.806
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |